Beyond contacts: the important role of the support region to distinguish stable and transient protein interfaces

Protein-protein interactions (PPIs) are fundamental to virtually all cellular processes; however, elucidating the principles that govern protein association into complexes remains a significant challenge. In this study, we present a comparative analysis of stable and transient protein interfaces, offering a detailed perspective on the interactions that form them. Moving beyond the traditional focus on pairs of neighboring residues, we examine interacting pairs by identifying their distinct non-bonded interactions. Additionally, we account for the contextual dependence of these interactions by analyzing the regions of the interface where they occur. Our approach quantifies the diversity of pairs in each region, considering the type of interface. Furthermore, we introduce an innovative strategy to analyze pair co-occurrence, enabling a comparison of the inner local organization of stable and transient interfaces. Our findings reveal that stable and transient interfaces differ not in overall residue composition, but in the residue- and interaction-partitioning patterns across the variably hydrated regions of the interface. These results underscore the importance of considering the contextual environment in which pairs interact and identify the support region as a key determinant for distinguishing transient and stable protein complexes. The software package developed for this analysis is available as open source.